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36 Open 68 Closed
36 Open 68 Closed
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Issues list

remove strand groups invalid This doesn't seem right
#258 opened Apr 17, 2024 by dave-doty
@lia-n2
matplotlib histogram of nearest neighbor energies closed in dev enhancement New feature or request
#255 opened Apr 4, 2024 by dave-doty
@dave-doty
merge Result and Evaluation
#254 opened Mar 26, 2024 by dave-doty
@lia-n2
allow subdomains to have multiple parents enhancement New feature or request
#252 opened Dec 15, 2023 by dave-doty
@lia-n2
1
generalized dependent domains enhancement New feature or request
#251 opened Dec 15, 2023 by dave-doty
@dave-doty
mismatches enhancement New feature or request
#250 opened Dec 15, 2023 by dave-doty
@dave-doty
2
do not require length parameter to Domain constructor when Domain.dependent is True and subdomains are independent invalid This doesn't seem right
#249 opened Dec 13, 2023 by dave-doty
find/use/compare black box stochastic local search optimization software
#247 opened Nov 6, 2023 by dave-doty
RNAplex output missing lines with sufficiently long input bug Something isn't working
#244 opened Oct 8, 2023 by dave-doty
use _normalize_domains_pairs_disjoint_parameters and _normalize_strands_pairs_disjoint_parameters enhancement New feature or request
#241 opened Sep 19, 2023 by dave-doty
prevent two strands with the same name bug Something isn't working
#228 opened Sep 30, 2022 by dave-doty
@lia-n2
remove declaration of private properties in classes invalid This doesn't seem right
#210 opened Jul 21, 2022 by dave-doty
@dave-doty
store StrandPair instead of Tuple[Strand, Strand] in ConstraintWithStrandPairs and make _determine_strand_pairs_to_check more efficient enhancement New feature or request
#209 opened Jul 21, 2022 by dave-doty
@dave-doty
dependent domains whose independent source is fixed should be fixed high priority invalid This doesn't seem right
#208 opened Jul 20, 2022 by dave-doty
@dave-doty
Allow inclusion of other arguments in description for constraints. enhancement New feature or request
#195 opened Jul 4, 2022 by cgevans
3
simplify API of evaluate function in constraint high priority invalid This doesn't seem right
#148 opened Dec 1, 2021 by dave-doty
create tool that allows design to be specified and pre-packaged constraints to be picked without writing Python code enhancement New feature or request
#147 opened Nov 28, 2021 by dave-doty
add more unit tests invalid This doesn't seem right
#140 opened Oct 17, 2021 by dave-doty
profile parallelism to see if speedups can be obtained enhancement New feature or request
#132 opened Oct 12, 2021 by dave-doty
add RNA parameter to pfunc and pre-packaged constraints enhancement New feature or request
#126 opened Sep 14, 2021 by dave-doty
allow quit early optimization even when there is positive probability to keep a higher-scoring change enhancement New feature or request
#124 opened Sep 14, 2021 by dave-doty
1
add tutorial documentation Improvements or additions to documentation high priority
#120 opened Sep 13, 2021 by dave-doty
incorporate O(n^2) time vectorized RNAduplex replacement for sequence pairs enhancement New feature or request
#89 opened Aug 23, 2021 by dave-doty
make independent fields private for Design/Strand/Domain, so that derived fields can be consistently recomputed by setters bug Something isn't working high priority
#78 opened Aug 18, 2021 by dave-doty
Check complex base pair probability in relation to other strands not part of the complex enhancement New feature or request
#32 opened Apr 7, 2021 by UnHumbleBen
1
ProTip! no:milestone will show everything without a milestone.